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Sergio Ruiz-Carmona
I am currently a Research Officer and Bioinformatician at the Baker Institute, under the supervision of professor Mike Inouye. My research interests are broad and involve mainly the relationship between genetic variants and their effect on protein structures.
I carried out my MSc and PhD in Barcelona in the Barril Lab, where I worked with different structure-based drug design methods with the aim to improve drug design for non-standard targets.
Education
PhD in Biomedicine
Universitat de Barcelona
Barcelona, ES
2017 - 2012
- Virtual Screening for novel MoA: Apps. and method developments
- Development and application of structure-based drug discovery methods
- Awards: Extraordinary prize for PhD Thesis and Ramon Margalef award for best publication
MSc in Bioinformatics for Health Sciences
Universitat Pompeu Fabra
Barcelona, ES
2012 - 2010
- Expanding Druggable Genome: PP-Interfaces as a new target class
- Study of novel rational approach to find PP interfacial binders
BSc in Biotechnology
Universitat Autònoma de Barcelona
Barcelona, ES
2010 - 2006
Research Experience
Research Officer and Bioinformatician
Inouye Lab
Baker Heart and Diabetes Institute
Melbourne, AU
Today - 2019
- I am working in a project that overlaps Structural Biology and Genomics, in collaboration with David Ascher’s Lab. Mainly, I am trying to understand how rare missense variants alter protein structures and can induce disease
- My role also involves giving Bioinformatics support to the whole institute, where I apply different statistical and data analysis methods in a wide range of projects, mainly related with cardiovascular diseases and diabetes
Postdoctoral Researcher
Barril Lab, Universitat de Barcelona
Barcelona, ES
2018 - 2017
- After finishing my PhD, I worked in exciting collaborative projects in the field of epigenetics and cancer, where I carried out multidisciplinary research and learned new experimental skills
EMBO Short-Term Fellow
Andreas Bender Lab, Unversity of Cambridge
Cambridge, GB
2017
- I spent 2 months in one of the main Pharmacogenomics groups in the world, where I used gene-expression profiles of different biological systems to study BRD4 and drug selectivity
- 2 months (Sep/Oct 2017) research stay. Funded by EMBO (also awarded FEBS Short-Term Fellowship)
MuTaLig COST Action Short-Term Fellow
Peter Kolb Lab, Philipps Universität Marburg
Marburg, DE
2017
- I applied the methods developed during my PhD, Dynamic Undocking, Docking and MD simulations, in order to find multipotent compounds targeting RNAse P of extremely pathogenic bacteria
- 1 month (Nov 2017) research stay. Funded by MuTaLig COST Action
Predoctoral Researcher
Barril Lab, Universitat de Barcelona
Barcelona, ES
2016 - 2011
- Master’s and PhD research projects in the Xavier Barril Lab
- I applied a combination of experimental and computational techniques to study non-standard drug targets. I also developed novel structure-based computational methods to help in identifying novel drugs
I have been working in several multidisciplinary research groups around the globe. I have applied a broad range of concepts and ideas in the drug discovery field (both experimental and computational) and also in genomics and data analysis
Skills and Training
Computational Techniques
Computer-Aided Drug Discovery (SBDD), Virtual Screening, Docking, Molecular Dynamics, Chemoinformatics, Quantum Chemistry, Bioinformatics Tools and Analysis
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Scientific Software
Bioinformatics software, pymol, openbabel, databases, molecular docking programmes and molecular modelling tools (Schrödinger, MOE)
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Programming
R, Python, Perl, C++, LaTeX, Bash, Java, MySQL, HTML and Android and Web Development
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Experimental Techniques
Biophysical Screening (SPR, DSF), Cell Growth, Protein Expression and Purification
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Selected Publications
I collaborated with different companies (Servier, Repsol and Vernalis) where I studied physicochemical properties of both small molecules and drug targets and also developed novel methods for virtual screening
Oxygen Pathway Limitations in Patients with Chronic Thromboembolic Pulmonary Hypertension
Circulation
Read it here
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2021
- Erin J Howden *, Sergio Ruiz-Carmona *, […] Andre La Gerche, Marion Delcroix and Guido Claessen
Dynamic Undocking: A Novel Method for Structure-Based Drug Discovery
Rational Drug Design (Book Chapter)
Read it here
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2018
- Maciej Majewski, Sergio Ruiz-Carmona and Xavier Barril
Dynamic undocking and the quasi-bound state as tools for drug discovery
Nature Chemistry
Read it here
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2017
- Sergio Ruiz-Carmona, P Schmidtke, […] Rod Hubbard and Xavier Barril
- Highlighted in its issue cover
Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR
Journal of Computer-Aided Molecular Design
Read it here
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2017
- Y Westermaier, Sergio Ruiz-Carmona, […] Pierre Ducrot and X Barril
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids
PLoS Computational Biology
Read it here
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2014
- Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, […] Xavier Barril, Rod Hubbard and S David Morley
I consider myself a passionate teacher. I have always volunteered and enrolled in as many teaching opportunities as possible during the different stages of my career
Teaching Experience
Introduction to R Course
Introduction to Stats Analyses Using R
Melbourne, AUS
2021
- 6h of online tutoring for Baker Heart and Diabetes Institute researchers
- Organized by Prof. Agus Salim and Dr. Gad Abraham
Associate Professor
Faculty of Pharmacy, Universitat de Barcelona
Barcelona, ES
2019 - 2015
- Classes in Pharmacy, Food Science and Nutrition degrees (total 400h)
Molecular Dynamics workshops
Novel methods for Drug Discovery
Marburg, DE
2017
- 6h theory and hands-on workshop for Dynamic Undocking and MDmix simulations. During my research visit at Kolb’s Lab
Drug Discovery workshop
Computer-aided Drug Design
Ciudad de Mexico, MX
2016
- Organized and imparted 30h of theory and hands-on sessions for researchers at the Instituto de Química (Chemistry Institute), at the UNAM
- With Profs. Xavier Barril and Axel Bidon-Chanal
Scientific Communications
I have also developed rDock and Barril Lab websites, used as dissemination platforms where the different tutorials and blog entries are shared with the community
Characterization of the effect of disease-causing genetic variants using protein 3D structural alterations
Lorne Proteins 2021
Virtual Poster Presentation
Lorne, AUS
2021
Var2Prot: A new tool to unravel the 3D structural effect of genetic variants
Lorne Proteins 2020
Oral Communication
Lorne, AUS
2020
Var2Prot: A new tool to unravel the 3D structural effect of genetic variants
GIW/ABACBS 2019
Poster Presentation
Sydney, AUS
2019
New approaches in SBDD: Applications to non-standard targets
Joint Klebe & Kolb Seminars
Invited Oral Communication
Marburg, DE
2017
Virtual Screening for novel mechanisms of action: Applications and method developments
Andreas Bender Lab Seminars
Invited Oral Communication
Cambridge, UK
2017
Dynamic Undocking and the Quasi-Bound State as Tools for Drug Discovery
7th Joint Sheffield Conference on Chemoinformatics
Oral Communication
Sheffield, UK
2016
Dynamic Undocking and the Quasi-Bound State as Tools for Drug Discovery
III Symposium of Young Researchers in Medicinal Chemistry
Oral Communication
Barcelona, ES
2016
Dynamic undocking of protein complexes: a new tool for ligand discovery
Gordon Research Conference: New Frontiers in CADD
Poster Presentation
Mount Snow (VT), USA
2015
rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
8th International Workshop on New Approaches in Drug Design
Poster Presentation
Marburg, DE
2014
Data Science Writing
rDock Docking Manuals and Tutorials
rDock website content
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2015 - 2012
- I developed and validated different tutorials for using rDock, with around 300 visits every month
Small Molecule Parametrization
Blog entry
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2013
- Blog entry about how to parametrize small molecules using Gaussian and AMBER forcefield, for Molecular Dynamic simulations
- 50 reads per month
Selected Press Stories
Australasian Leadership Computing Grants
Story about NCI Computing Grant
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2021 - 2020
- Together with Mike Inouye, we were awarded a 1 year computing grant by the Australian National Compuational Infrastructure to study COVID-19 proteins and possible drug treatments
Dynamic Undocking paper publication
News about our publication and selection for cover
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2017
- Highlight from Universitat de Barcelona about our Dynamic Undocking publication in Nature Chemistry and its selection for the March 2017 printed cover